fFitAndPlot <- function (dat,
model1,
model2,
model3,
model4,
model5,
model6)
{
fit1 <- fFitModel(model1, dat)
fit2 <- fFitModel(model2, dat)
fit3 <- fFitModel(model3, dat)
fit4 <- fFitModel(model4, dat)
fit5 <- fFitModel(model5, dat)
fit6 <- fFitModel(model6, dat)
loo1 <- loo::loo(fit1$fit, save_psis = TRUE, 'logLikelihood')
loo2 <- loo::loo(fit2$fit, save_psis = TRUE, 'logLikelihood')
loo3 <- loo::loo(fit3$fit, save_psis = TRUE, 'logLikelihood')
loo4 <- loo::loo(fit4$fit, save_psis = TRUE, 'logLikelihood')
loo5 <- loo::loo(fit5$fit, save_psis = TRUE, 'logLikelihood')
loo6 <- loo::loo(fit6$fit, save_psis = TRUE, 'logLikelihood')
comparison <- data.frame(round(loo::loo_compare(x = list(loo1, loo2, loo3, loo4, loo5, loo6)), 3)) [, 1:2]
pp1 <- fPlotModel(fit1, dat, 'model 1', 'constant foi')
pp2 <- fPlotModel(fit2, dat, 'model 2', 'continuous')
pp3 <- fPlotModel(fit3, dat, 'model 3', 'Student t ')
pp4 <- fPlotModel(fit4, dat, 'model 4', 'contin. unsmoothed')
pp5 <- fPlotModel(fit5, dat, 'model 5', 'laplace')
pp6 <- fPlotModel(fit6, dat, 'model 6', 'Salje')
ppC <-
ggplot(data.frame(x= 0:1, y = 0:1), aes(x, y)) +
geom_blank() + ylab('') + xlab ('') + theme_void() +
annotation_custom(tableGrob(comparison))
res_survey <- list(dat = dat,
fit1 = fit1,
fit2 = fit2,
fit3 = fit3,
fit4 = fit4,
fit5 = fit5,
fit6 = fit6,
comparison = comparison,
pp1 = pp1,
pp2 = pp2,
pp3 = pp3,
pp4 = pp4,
pp5 = pp5,
pp6 = pp6,
ppC = ppC
)
return(res_survey)
}
# ---- Datasets
# ---- Datasets
dat0 <- readRDS('data/chik_serop_feb2019.RDS') %>% mutate(counts = pos)
dat0 <- filter(dat0, survey != 'S078') # removed S078 as it only got one age class
datasets <- unique(dat0$survey)
for (s in datasets[47:85])
{
dat <- filter(dat0, survey == s) %>% arrange(age_mean_f)
res <- fFitAndPlot(dat, model1, model2, model3, model4, model5, model6)
saveRDS(res, paste0('res/', s, '.RDS' ))
gridExtra::grid.arrange(res$pp1, res$pp2, res$pp3,
res$pp4, res$pp5, res$pp6, res$ppC,
nrow = 1)
grid.rect(width = 1, height = 1, gp = gpar(lwd = 2, col = "blue", fill = NA))
rm(dat, res)
}
